GapMind for catabolism of small carbon sources

 

Alignments for a candidate for pgmA in Methanococcus aeolicus Nankai-3

Align Phosphoglucomutase/phosphomannomutase; PGM/PMM; EC 5.4.2.2; EC 5.4.2.8 (characterized)
to candidate WP_011973151.1 MAEO_RS02160 phosphoglucosamine mutase

Query= SwissProt::Q68BJ6
         (456 letters)



>NCBI__GCF_000017185.1:WP_011973151.1
          Length = 452

 Score =  309 bits (792), Expect = 1e-88
 Identities = 178/466 (38%), Positives = 274/466 (58%), Gaps = 33/466 (7%)

Query: 3   KLFGTFGVRGIANEEITPEFALKIGMAFGTLLKREGRERPLVVVGRDTRVSGEMLKDALI 62
           KLFGT G+R    + +TPE A K+G A   + K        VVVGRDTR +G++++++L 
Sbjct: 2   KLFGTSGIR---MKNLTPEIAYKVGFAVSQIAKN-------VVVGRDTRTTGDLIRNSLF 51

Query: 63  SGLLSTGCDVIDVGIAPTPAIQWATNHFNADGGAVITASHNPPEYNGIKLLEPNGMGLKK 122
           +GLL+ G +++D+GI PTP + ++  ++  D G +ITASHNP EYNGIKL   +G   + 
Sbjct: 52  AGLLNGGAEIVDIGIVPTPTLGYSARNY--DMGIMITASHNPSEYNGIKLFNKDGTSFRP 109

Query: 123 EREAIVEELFFSE-DFHRAKWNEIGEL-RKEDIIKPYIEAIKNRVDVEAIKKRRPFVVVD 180
           E+E  +E++ +++ +  R  WN I ++   E  +K Y + I + V++     +   VVVD
Sbjct: 110 EQEQNIEDIIYNKKNQKRVSWNSIKKVWTDESALKKYSDFILDSVEIN----KNFSVVVD 165

Query: 181 TSNGAGSLTLPYLLRELGCKVVSVNAHPDGHFPARNPEPNEENLKGFMEIVKALGAD--- 237
            +N AG +  PYL  ++G  V+SVN H DG F  R+PEPNE+NL+  M ++K L  +   
Sbjct: 166 CANSAGCVASPYLFTDVGAHVISVNGHIDGRFIGRSPEPNEKNLQDTMHMIKGLNENNKG 225

Query: 238 ---FGVAQDGDADRAVFIDENGRFIQGDKTFALVADAVLRENGGGLLVTTIATSNLLDDI 294
               G+A DGDADR + IDE GR    DK  A+ +  +  + G   ++TT+  S  +++ 
Sbjct: 226 NKYIGIAHDGDADRMIAIDEKGRLTDFDKLLAVFSRYMAEKTGTKTIITTVDASMAIEEY 285

Query: 295 AKRNGAKVMRTKVGDLIVARALLENNGTI-GGEENGGVIFPDFVLGRDGAMTTAKIVEIF 353
            K     V+RTKVGD+ V+  L +++  I GGE +G  I  D  L  DG ++  +++E+ 
Sbjct: 286 LKDLNVNVIRTKVGDVAVSDELNKHDDAIFGGEPSGTWIHKDIHLTPDGILSGLRLLEMM 345

Query: 354 AKSGKKFSELIDELPKYYQFKTKRHVEGDRKAIVAKVAELAEKKG-----YKIDTTDGTK 408
               KK  ELID++P Y   + K     D+K I   V +   K G      +++T DG +
Sbjct: 346 EFYDKKLYELIDDVPCYSNLREKLPCPDDKKII---VMDFVIKNGENIFDAEVETIDGAR 402

Query: 409 IIFDDGWVLVRASGTEPIIRIFSEAKSEEKAREYLELGIKLLEEAL 454
              DDGWVL+R SGTEP +R+  EAK++  A+E LE GIKL+++ L
Sbjct: 403 FSLDDGWVLIRPSGTEPFVRVRVEAKNDIIAKELLEKGIKLVKDGL 448


Lambda     K      H
   0.317    0.139    0.396 

Gapped
Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 1
Number of Hits to DB: 597
Number of extensions: 35
Number of successful extensions: 7
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 1
Number of HSP's successfully gapped: 1
Length of query: 456
Length of database: 452
Length adjustment: 33
Effective length of query: 423
Effective length of database: 419
Effective search space:   177237
Effective search space used:   177237
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 51 (24.3 bits)

This GapMind analysis is from Apr 09 2024. The underlying query database was built on Sep 17 2021.

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About GapMind

Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.

A candidate for a step is "high confidence" if either:

where "other" refers to the best ublast hit to a sequence that is not annotated as performing this step (and is not "ignored").

Otherwise, a candidate is "medium confidence" if either:

Other blast hits with at least 50% coverage are "low confidence."

Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:

GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).

For more information, see:

If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know

by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory